Biology subjects

Nishihara, A.

Publications and source records attributed to Nishihara, A..

3 recordsLinked to original sources

bioRxiv2026

Epigenomes in thermophilic microbial communities and their impact on the interaction across prokaryotes and mobilomes

DNA chemical modifications, including methylation, are widespread in prokaryotes and mobilomes, including viruses, plasmids, and other extrachromosomal DNAs, and play important roles in their ecology and interactions. However, current knowledge of these modification systems and their association with interactions between hosts and mobilomes across communities, including those in extreme environments, is severely limited. Here, using single-molecule real-time sequencing and single-cell genome sequencing technologies, we conducted a culture-independent metaepigenomic analysis of microbial communities in hot spring biofilms. A total of 248, 332, and 465 genomes were constructed from diverse prokaryotes, viruses, and extrachromosomal circular DNAs, respectively, from 10 biofilm samples collected from 3 hot spring sites. In total, 1106 candidate methylated motifs and 3280 genes associated with the restriction-modification (RM) system, including DNA methyltransferases (MTases), were identified. In contrast to the varied methylated motifs, the nucleotide-level modification ratios were consistent with those of a common Escherichia coli genome, and an environment-dependent epigenomic preference attributed to the lack of C5-methylcytosine was observed, as supported by direct measurements of modified bases by liquid chromatography-tandem mass spectrometry. A systematic survey revealed various defense systems in the genome, and almost half of the MTase genes were estimated to be genetically involved in defense mechanisms against extracellular DNA, such as RM systems. The mobilomes and their predicted hosts shared epigenomic patterns within each interactive subnetwork, suggesting that mobilome DNA was modified by host MTase during the current infection or transfection, rather than serving as historical records. Our findings highlight that DNA modification shapes multiple ecological and evolutionary strategies in interactions between prokaryotes and mobilomes, and that epigenomes serve as a potential signature for accurate prediction of current host-phage interactions.

microbiology↗

bioRxiv2025

Exploring the diversity and physiological characteristics of RubisCO-mediated carbon fixation in culturable prokaryotes

The utilization of microbial resources requires their relevant reproducible characteristics, and genome analysis plays a crucial role in discovering valuable strains for future applications. In this study, we analyzed potential carbon-fixing microorganisms via Calvin-Benson-Bassham (CBB) cycle using 6,262 bacterial and 487 archaeal genomes from available cultures in Japan Collection of Microorganisms (JCM), one of the well-established culture collections today. A total of 306 strains (147 genera, eight phyla) carried CBB cycle genes and a literal survey showed that 74 genera had reported evidence of their autotrophic growth, although 73 lacked supporting information. Phylogenetic analysis of RubisCO large subunit (RbcL) identified diverse forms (IA, IB, IC, IE, I+, II, and III) with distinct metabolic associations: form IA associated with sulfur oxidation and form IC with hydrogen oxidation. Genome-based metabolic predictions suggested potential carbon fixation in numerous strains lacking experimental evidence. Our analyses showed members of Actinomycetota harboring form IE RubisCO tend to associate with hydrogen oxidation possibly using oxygen or nitrate as an electron acceptor. Additionally, 12 strains in Pseudomonadota contained pufL and pufM genes, suggesting possible phototrophic capabilities, although some failed to predict their electron donors and they possibly use CBB cycle to regulate intracellular redox balance under photoheterotrophic growth. Our findings highlight unrecognized autotrophic potentials in JCM strains and expand our knowledge of carbon fixation diversity. Future experimental validation will deepen our understanding of these microbes roles in the global carbon cycle, with potential applications in carbon sequestration and environmental sustainability.

microbiology↗

bioRxiv2024

Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus

Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here Candidatus Methanobrevibacter cononymphae, is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0 to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, Ca. Methanobrevibacter cononymphae is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of Ca. Methanobrevibacter cononymphae showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.

microbiology↗